Integrating transcription kinetics with alternative polyadenylation and cell cycle control

Moreira, Alexandra

doi:10.4161/nucl.2.6.18064

Cited by 10 publications

(6 citation statements)

References 49 publications

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“…Interestingly, the authors found that slow transcription elongation facilitates the use of weak PASs, not necessarily restricted to the canonical AAUAAA motif. These observations support the kinetic coupling model, according to which the choice of PAS depends on the elongating speed of RNAPII (Moreira, 2011). Comparable observations were made in yeast while studying the end formation of non-coding transcripts, which depends on the Nrd1-Nab3-Sen1 (NNS) complex.…”

Section: Choice Of Polyadenylation Sitesupporting

confidence: 71%

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

Slobodin

Dikstein

2020

EMBO Reports

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Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine‐tuning of gene expression and the adjustment to constantly changing conditions.

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Section: Choice Of Polyadenylation Sitesupporting

confidence: 71%

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

Slobodin

Dikstein

2020

EMBO Reports

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“…Transcription elongation rates have also been demonstrated to affect poly(A) site selection (22,23). The proposed model is that slower transcription elongation allows more time for the termination complex to cleave at the ‘weaker’ promoter-proximal poly(A) site (22,59).…”

Section: Discussionmentioning

confidence: 99%

UV damage regulates alternative polyadenylation of the RPB2 gene in yeast

Volkert

2013

Nucleic Acids Research

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Alternative polyadenylation (APA) is conserved in all eukaryotic cells. Selective use of polyadenylation sites appears to be a highly regulated process and contributes to human pathogenesis. In this article we report that the yeast RPB2 gene is alternatively polyadenylated, producing two mRNAs with different lengths of 3′UTR. In normally growing wild-type cells, polyadenylation preferentially uses the promoter-proximal poly(A) site. After UV damage transcription of RPB2 is initially inhibited. As transcription recovers, the promoter-distal poly(A) site is preferentially used instead, producing more of a longer form of RPB2 mRNA. We show that the relative increase in the long RPB2 mRNA is not caused by increased mRNA stability, supporting the preferential usage of the distal poly(A) site during transcription recovery. We demonstrate that the 3′UTR of RPB2 is sufficient for this UV-induced regulation of APA. We present evidence that while transcription initiation rates do not seem to influence selection of the poly(A) sites of RPB2, the rate of transcription elongation is an important determinant.

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“…Alternative polyadenylation influences the coding region, stability, and localization and translation efficiency of mRNA [42]. Thus, it can regulate gene expression to control various plant developmental processes, such as floral organ identity [43,44,[52][53][54]. Most of the DEGs associated with RNA splicing and polyadenylation showed sex-biased expression ( Fig.…”

Section: Full-length Transcriptome Analysismentioning

confidence: 99%

Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L

Meng

Mei

et al. 2020

BMC Genomics

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Background Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, comparative transcriptome analysis of male and female flowers were performed to explore the sex differentiation mechanism in spinach. Results Compared with published genome of spinach, 10,800 transcripts were newly annotated; alternative splicing, alternative polyadenylation and lncRNA were analyzed for the first time, increasing the diversity of spinach transcriptome. A total of 2965 differentially expressed genes were identified between female and male flowers at three early development stages. The differential expression of RNA splicing-related genes, polyadenylation-related genes and lncRNAs suggested the involvement of alternative splicing, alternative polyadenylation and lncRNA in sex differentiation. Moreover, 1946 male-biased genes and 961 female-biased genes were found and several candidate genes related to gender development were identified, providing new clues to reveal the mechanism of sex differentiation. In addition, weighted gene co-expression network analysis showed that auxin and gibberellin were the common crucial factors in regulating female or male flower development; however, the closely co-expressed genes of these two factors were different between male and female flower, which may result in spinach sex differentiation. Conclusions In this study, 10,800 transcripts were newly annotated, and the alternative splicing, alternative polyadenylation and long-noncoding RNA were comprehensively analyzed for the first time in spinach, providing valuable information for functional genome study. Moreover, candidate genes related to gender development were identified, shedding new insight on studying the mechanism of sex determination and differentiation in plant.

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Integrating transcription kinetics with alternative polyadenylation and cell cycle control

Cited by 10 publications

References 49 publications

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

UV damage regulates alternative polyadenylation of the RPB2 gene in yeast

Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L

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